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Qu W, Wang F, Sun D, Liu Y, Jin X, Gong Z, Liu J, Zhang N, Wen D, Wang C, Jia H, Xu R, Tang X, Chen S, Fu X, Li X, Rong H, Zhang T, Jin C, Chen L, Li J, Liu Y, Cai J, Jiang B, Zha L. Internal validation of the GA118-24B Genetic Analyzer, a stable capillary electrophoresis system for forensic DNA identification. Int J Legal Med 2024; 138:361-373. [PMID: 37843624 DOI: 10.1007/s00414-023-03106-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023]
Abstract
The GA118-24B Genetic Analyzer (hereafter, "GA118-24B") is an independently developed capillary electrophoresis instrument. In the present research, we designed a series of validation experiments to test its performance at detecting DNA fragments compared to the Applied Biosystems 3500 Genetic Analyzer (hereafter, "3500"). Three commercially available autosomal short tandem repeat multiplex kits were used in this validation. The results showed that GA118-24B had acceptable spectral calibration for three kits. The results of accuracy and concordance studies were also satisfactory. GA118-24B showed excellent precision, with a standard deviation of less than 0.1 bp. Sensitivity and mixture studies indicated that GA118-24B could detect low-template DNA and complex mixtures as well as the results generated by 3500 in parallel experiments. Based on the experimental results, we set specific analytical and stochastic thresholds. Besides, GA118-24B showed superiority than 3500 within certain size ranges in the resolution study. Instead of conventional commercial multiplex kits, GA118-24B performed stably on a self-developed eight-dye multiplex system, which were not performed on 3500 Genetic Analyzer. We compared our validation results with those of previous research and found our results to be convincing. Overall, we conclude that GA118-24B is a stable and reliable genetic analyzer for forensic DNA identification.
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Affiliation(s)
- Weifeng Qu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Feng Wang
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Dan Sun
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Yi Liu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Xin Jin
- Public Security Department of Hainan Province, No. 9. Binya Road, Hainan, 570203, China
| | - Zheng Gong
- Criminal Technology Detachment, Public Security Bureau of Harbin, No. 35. Dongfeng Road, Harbin, 150010, China
| | - Jinjie Liu
- Criminal Investigation Detachment, Public Security Bureau of Beijing, No. 44. Banbuqiao Road, Beijing, 102611, China
| | - Ningjie Zhang
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Dan Wen
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Chudong Wang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Hongtao Jia
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Ruyi Xu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Xuan Tang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Siqi Chen
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Xiaoyi Fu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Xue Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Haibo Rong
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Tao Zhang
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Chuan Jin
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Li Chen
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China
| | - Jienan Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Ying Liu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Jifeng Cai
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China
| | - Bowei Jiang
- Ministry of Public Security of P.R.C., The First Research Institute, No. 1. Shouti South Road, Beijing, 100044, China.
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No. 172. Tongzipo Road, Changsha, 410013, China.
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Guo LL, Yuan JH, Zhang C, Zhao J, Yao YR, Guo KL, Meng Y, Ji AQ, Kang KL, Wang L. Developmental validation of the STRSeqTyper122 kit for massively parallel sequencing of forensic STRs. Int J Legal Med 2024:10.1007/s00414-024-03195-2. [PMID: 38416217 DOI: 10.1007/s00414-024-03195-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/09/2024] [Indexed: 02/29/2024]
Abstract
Massively parallel sequencing allows for integrated genotyping of different types of forensic markers, which reduces DNA consumption, simplifies experimental processes, and provides additional sequence-based genetic information. The STRseqTyper122 kit genotypes 63 autosomal STRs, 16 X-STRs, 42 Y-STRs, and the Amelogenin locus. Amplicon sizes of 117 loci were below 300 bp. In this study, MiSeq FGx sequencing metrics for STRseqTyper122 were presented. The genotyping accuracy of this kit was examined by comparing to certified genotypes of NIST standard reference materials and results from five capillary electrophoresis-based kits. The sensitivity of STRseqTyper122 reached 125 pg, and > 80% of the loci were correctly called with 62.5 pg and 31.25 pg input genomic DNA. Repeatability, species specificity, and tolerance for DNA degradation and PCR inhibitors of this kit were also evaluated. STRseqTyper122 demonstrated reliable performance with routine case-work samples and provided a powerful tool for forensic applications.
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Affiliation(s)
- Li-Liang Guo
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Jia-Hui Yuan
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Chi Zhang
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Jie Zhao
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Yi-Ren Yao
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Ke-Li Guo
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Yang Meng
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - An-Quan Ji
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
| | - Ke-Lai Kang
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
| | - Le Wang
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China.
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3
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Chen L, Wang L, Zeng Y, Yin D, Tang F, Xie D, Zhu H, Li L, Wang J. A prenatal case misunderstood as specimen confusion: 46,XY/46,XY chimerism. BMC Pregnancy Childbirth 2024; 24:126. [PMID: 38347456 PMCID: PMC10860253 DOI: 10.1186/s12884-024-06321-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/05/2024] [Indexed: 02/15/2024] Open
Abstract
Chimerism results from the fusion of two zygotes in a single embryo, whereas mosaicism results from mitotic errors in a single zygote. True human chimerism is rare, with fewer than 100 cases reported in the literature. Here, we report a case in which the fetus was identified as having tetragametic chimerism based on short tandem repeat - polymerase chain reaction analysis of the family observed during amniocentesis for advanced maternal age. The chimerism occurred via the fertilization of two ova by two spermatozoa, followed by the fusion of early embryos. The genotypes of the two amniotic fluid samples obtained successively by one puncture were completely different, and the sex chromosomes were XY. Karyotyping and copy number variation sequencing showed no abnormalities. The fetus was delivered at term and the phenotype of the newborn was normal.
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Affiliation(s)
- Lin Chen
- Department of Medical Genetics / Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou District, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, 610041, China
| | - Li Wang
- Department of Medical Genetics / Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou District, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, 610041, China
| | - Yang Zeng
- Department of Medical Genetics / Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou District, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, 610041, China
| | - Daishu Yin
- Department of Medical Genetics / Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou District, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, 610041, China
| | - Feng Tang
- Department of Medical Genetics / Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou District, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, 610041, China
| | - Dan Xie
- Department of Medical Genetics / Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou District, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, 610041, China
| | - Hongmei Zhu
- Department of Medical Genetics / Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou District, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, 610041, China
| | - Lingping Li
- Department of Medical Genetics / Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou District, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, 610041, China
| | - Jing Wang
- Department of Medical Genetics / Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou District, Chengdu, 610041, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, 610041, China.
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4
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Alizadeh S, Khamse S, Tajeddin N, Khorram Khorshid HR, Delbari A, Ohadi M. A GCC repeat in RAB26 undergoes natural selection in human and harbors divergent genotypes in late-onset Alzheimer's disease. Gene 2024; 893:147968. [PMID: 37931854 DOI: 10.1016/j.gene.2023.147968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/28/2023] [Accepted: 11/03/2023] [Indexed: 11/08/2023]
Abstract
Although mainly located in genic regions and being mutation hotspots, intact blocks of CG-rich trinucleotide short tandem repeats (STRs) are largely overlooked with respect to their link with natural selection. The human RAB26 (member RAS oncogene family) directs synaptic and secretory vesicles into preautophagosomal structures, inhibition of which specifically disrupts axonal transport of degradative organelles and leads to an axonal dystrophy, resembling Alzheimer's disease (AD). Human RAB26 contains a GCC repeat in the top 1st percent in respect of length. Here we sequenced this STR in 441 Iranian individuals, consisting of late-onset neurocognitive disorder (NCD) (N = 216) and controls (N = 225). In both groups, the 12-repeat allele and the 12/12 genotype were predominantly abundant. We found excess of homozygosity for non-12 alleles in the NCD group (Mid-P exact = 0.027). Furthermore, divergent genotypes were detected that were specific to the NCD group (2.8% of genotypes) (Mid-P exact = 0.006) or controls (3.1% of genotypes) (Mid-P exact = 0.004). The patients harboring divergent genotypes received the diagnosis of AD. Based on the predominant abundance of the 12-repeat and 12/12 genotype in both groups, excess of non-12 homozygosity in the NCD group, and divergent genotypes across the NCD and control groups, we propose natural selection at this locus and link with late-onset AD. Our findings strengthen the hypothesis that a collection of rare genotypes unambiguously contribute to the pathogenesis of late-onset NCDs, such as AD.
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Affiliation(s)
- S Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - S Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - N Tajeddin
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - H R Khorram Khorshid
- Personalized Medicine and Genometabolomics Research Center, Hope Generation Foundation, Tehran, Iran
| | - A Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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Wang Z, Song M, Lyu Q, Ying J, Wu Q, Song F, Jiang L, Wei X, Wang S, Wang F, Zhou Y, Song X, Luo H. A forensic population database of autosomal STR and X-STR markers in the Qiang ethnic minority of China. Heliyon 2023; 9:e21823. [PMID: 38034634 PMCID: PMC10685182 DOI: 10.1016/j.heliyon.2023.e21823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
The Qiang ethnic group is one of the oldest ethnic groups in China and is the most active ethnic group among all the populations along the Tibetan-Yi corridor. They have had a profound impact nationally and internationally. The paternal and maternal genetic feature of the Qiang ethnic group has been revealed, leaving the question of the genetic characteristics from autosomes and X chromosome not answered. The aim of this study was to explore the potential of 36 A-STR (Microreader™ 36A ID System) and 19 X-STR (Microreader™ 19X System) for application in the Qiang population and to elucidate their genetic diversity in southwest China. The cumulative probability of exclusion (CPE) for autosomal STRs is 1-1.3814 × 10-15 and the mean paternity exclusion chance (MEC) for X-STRs is 1-1.7323 × 10-6. Forensic parameters suggest that the STRs analyzed here are well-suited for forensic applications. The results of phylogenetic, interpopulation differentiation, and principal coordinates analysis (PCoA) indicate that the Qiang people have extensive connections with ethnic minorities in China, supporting the view that the Qiang people are the oldest group in the entire Sino-Tibetan language family. The Qiang appeared genetically more associated with most ethnic groups in China, especially the Han. The calculation of random matching probability (RMP) was improved by Fst correction of allele frequencies to make RMP more accurate and reasonable. This study can fill in the gaps in the Qiang STR reference database, providing valuable frequency data for forensic applications and evidence for the Qiang's genetic pattern as an important ancestral position in the Sino-Tibetan populations.
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Affiliation(s)
- Zefei Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Mengyuan Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiang Lyu
- Department of Clinical Laboratory, People's Hospital of Beichuan Qiang Autonomous County, Beichuan, 622750, China
| | - Jun Ying
- Department of Clinical Laboratory, Santai People's Hospital, Santai, 621100, China
| | - Qian Wu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Lanrui Jiang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Xiaowen Wei
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Shuangshuang Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Fei Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Xingbo Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
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João D, Cardoso S, Monteiro P, Leal C, Bartosch C. Short tandem repeat analysis: a practical tool to identify specimen mix-ups in the pathology laboratory. Virchows Arch 2023; 483:549-554. [PMID: 37369928 DOI: 10.1007/s00428-023-03578-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/22/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023]
Abstract
Despite all precautions in pathology laboratories, contaminations and specimen mix-ups still occur and can negatively impact both patients and institutions. We present two cases in which short tandem repeat (STR) analysis was used to assert the correct identity of specimens. The first patient had a biopsy diagnosis of triple negative invasive carcinoma of no special type of the breast. Sample mix-up with another biopsy was suspected, because in her post-chemotherapy mastectomy specimen, a hormone receptor-positive lobular carcinoma was diagnosed. STR analysis displayed a complete common loci profile of the patient's biopsy and mastectomy, supporting that no mix-up occurred. The second patient underwent hysterectomy due to cervix squamous cell carcinoma. A fragment of adenocarcinoma was identified and confirmed by STR profile to be a contaminant. STR analysis is a fast, easy-to-perform, and widely available technique which can clarify contaminations and specimen mix-ups in pathology laboratories.
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Affiliation(s)
- David João
- Department of Pathology, Centro Hospitalar de Vila Nova de Gaia/Espinho, Porto, Portugal.
| | - Sara Cardoso
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Paula Monteiro
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Conceição Leal
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Carla Bartosch
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal
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7
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Chen YH, Connelly JP, Florian C, Cui X, Pruett-Miller SM. Short tandem repeat profiling via next-generation sequencing for cell line authentication. Dis Model Mech 2023; 16:dmm050150. [PMID: 37712227 PMCID: PMC10618599 DOI: 10.1242/dmm.050150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023] Open
Abstract
Cell lines are indispensable models for modern biomedical research. A large part of their usefulness derives from the ability of a cell line to proliferate over multiple passages (often indefinitely), allowing multiple experiments to be performed. However, over time, cell line identity and purity can be compromised by human errors. Cross-contamination from other cell lines and complete misidentification are both possible. Routine cell line authentication is a necessary preventive measure and has become a requirement for many funding applications and publications. Short tandem repeat (STR) profiling is the most common method for cell line authentication and is usually carried out using standard polymerase chain reaction-capillary electrophoresis analysis (STR-CE). Here, we evaluated next-generation sequencing (NGS)-based STR profiling of human and mouse cell lines at 18 and 15 loci, respectively, in a high-throughput format. Using the Python program STRight, we demonstrate that NGS-based analysis (STR-NGS) is superior to standard STR-CE in terms of the ability to report the sequence context of repeat motifs, sensitivity and flexible multiplexing capability. STR-NGS is thus a valuable alternative for cell line authentication.
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Affiliation(s)
- Yi-Hsien Chen
- Genome Engineering & Stem Cell Center (GESC@MGI), Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Jon P. Connelly
- Center for Advanced Genome Engineering (CAGE), Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Colin Florian
- Genome Engineering & Stem Cell Center (GESC@MGI), Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Xiaoxia Cui
- Genome Engineering & Stem Cell Center (GESC@MGI), Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Shondra M. Pruett-Miller
- Center for Advanced Genome Engineering (CAGE), Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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8
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Wang Y, Hou X, Liu Q, Wang D, Li S, Dang Z. Verification of a loss of heterozygosity at the D8S1179 locus in a paternity case by the MiSeq FGx system. Int J Legal Med 2023; 137:1407-1412. [PMID: 37338606 DOI: 10.1007/s00414-023-03043-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 06/07/2023] [Indexed: 06/21/2023]
Abstract
Capillary electrophoresis is widely used to study short tandem repeats (STRs) in forensic genetics. However, next-generation sequencing platforms have become a new strategy for forensic DNA typing. In this study, we report a false four-step STR mutation between an alleged father (AF) and child in a paternity case. A total of 23 autosomal STR loci were evaluated using the Huaxia™ Platinum and Goldeneye™ 20A kits, revealing a single mismatch in D8S1179 between the AF (10/10) and the male child (14/14). Additional Y-STR typing of the AF and child was performed, and the results were consistent with those based on 27 Y-STR loci. To further confirm the experimental results, we sequenced the individuals using the MiSeq FGx system and detected 10/15 unbalanced alleles in the D8S1179 locus of the AF and 14/15 unbalanced alleles in the D8S1179 locus of the child. Sanger sequencing revealed that both the AF and child had the C→G point mutation in the primer binding region of D8S1179 resulting in allelic dropout. Therefore, the verification of STR typing by different sequencing systems is helpful for the interpretation of results in cases of multistep STR mutations.
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Affiliation(s)
- Yequan Wang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, Shandong, People's Republic of China.
- Forensic Science Center of Jining Medical University, Jining, Shandong, People's Republic of China.
| | - Xiudi Hou
- Forensic Science Center of Jining Medical University, Jining, Shandong, People's Republic of China
| | - Qi Liu
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, Shandong, People's Republic of China
- Forensic Science Center of Jining Medical University, Jining, Shandong, People's Republic of China
| | - Dan Wang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, Shandong, People's Republic of China
- Forensic Science Center of Jining Medical University, Jining, Shandong, People's Republic of China
| | - Shuyue Li
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, Shandong, People's Republic of China
- Forensic Science Center of Jining Medical University, Jining, Shandong, People's Republic of China
| | - Zhen Dang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, Shandong, People's Republic of China.
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9
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Spruijtenburg B, Meijer EFJ, Xiao M, Shawky SM, Meis JF, de Groot T, El-Kholy MA. Genotyping and susceptibility testing uncovers large azole-resistant Candida tropicalis clade in Alexandria, Egypt. J Glob Antimicrob Resist 2023; 34:99-105. [PMID: 37419181 DOI: 10.1016/j.jgar.2023.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/09/2023] [Accepted: 06/28/2023] [Indexed: 07/09/2023] Open
Abstract
OBJECTIVES Candida tropicalis is an emerging medically relevant Candida species. The yeast primarily causes opportunistic infections in intensive care units and is highly prevalent in tropical countries. The genetic diversity within this species is high, and nosocomial transmission has been reported. C. tropicalis genotyping of isolates from low- and middle-income countries is underrepresented when compared with that from high-income countries. Also, in Egypt, only limited genotyping has been conducted for C. tropicalis isolates, while antifungal resistance seems to increase, especially against azoles. METHODS Antifungal susceptibility testing was performed on 64 C. tropicalis isolates from ICU patients collected from multiple hospitals in Alexandria, Egypt. Genotyping by means of short tandem repeat (STR) and whole genome sequencing (WGS) single nucleotide polymorphism (SNP) analysis was performed. RESULTS Using antifungal susceptibility testing, fluconazole resistance was observed in 24 isolates (38%), of which 23 harboured an ERG11 G464S substitution, previously shown to cause resistance in Candida albicans. STR genotyping showed that these 23 isolates were related, forming a distinct resistant clade. WGS SNP analysis subsequently confirmed this genetic relationship, although isolates within this clade differed in at least 429 SNPs, suggesting that these were independently introduced. CONCLUSION Overall, STR and WGS SNP analysis of this collection indicates limited C. tropicalis nosocomial transmission in Alexandria, while the presence of this large azole-resistant C. tropicalis clade within this city hampers the treatment of intensive care unit patients.
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Affiliation(s)
- Bram Spruijtenburg
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; Center of Expertise in Mycology Radboud University Medical Center/Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Eelco F J Meijer
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; Center of Expertise in Mycology Radboud University Medical Center/Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Meng Xiao
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, People's Republic of China
| | - Sherine M Shawky
- Department of Microbiology, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Jacques F Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; Center of Expertise in Mycology Radboud University Medical Center/Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; Department I of Internal Medicine, University of Cologne, Excellence Center for Medical Mycology, Cologne, Germany
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands; Center of Expertise in Mycology Radboud University Medical Center/Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Mohammed A El-Kholy
- Department of Microbiology and Biotechnology, Division of Clinical and Biological Sciences, College of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), Alexandria, Egypt.
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10
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Sathirapatya T, Worrapitirungsi W, Sukawutthiya P, Noh H, Pitiwararom R, Vongpaisarnsin K. The concordance of length- and sequence-based STRs used in forensic markers with guidance for practice. Forensic Sci Int 2023; 348:111729. [PMID: 37196610 DOI: 10.1016/j.forsciint.2023.111729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/19/2023]
Abstract
Next-generation sequencing (NGS) technology has shed light on every aspect of genetic discoveries, including forensic genetics. The Miseq® FGx Forensic Genetic System (Verogen) is one of the pioneering forensic NGS that provided a complete system from library preparation to data analysis. The system has been validated by several studies and led to a more practical aspect. Short tandem repeat (STR) is a well-established marker that was designed specifically for human individualization. Since NGS provides different data from fragment analysis, a new STR nomenclature is established to make NGS backward compatible with the previous data. In this study, Thai population were used to evaluate the Miseq® FGx Forensic genetic system (Verogen) in practical aspect, including concordance study and forensic population parameters. In summary, we purposed a practical guideline for sequence-based STRs.
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Affiliation(s)
- Tikumphorn Sathirapatya
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Forensic Genetic Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Wikanda Worrapitirungsi
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Forensic Genetic Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Poonyapat Sukawutthiya
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Forensic Genetic Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Hasnee Noh
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Forensic Genetic Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Rachtipan Pitiwararom
- Faculty of Criminology and Justice Administration, Rangsit University, Pathum Thani, Thailand
| | - Kornkiat Vongpaisarnsin
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand; Forensic Genetic Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
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11
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Yang L, Fu J, Cheng J, Zhou B, Chen M, Anuchapreeda S, Fu J. Novel, heterozygous, de novo pathogenic variant (c.4963delA: p.Thr1656Glnfs*42) of the NF1 gene in a Chinese family with neurofibromatosis type 1. BMC Med Genomics 2023; 16:85. [PMID: 37095468 PMCID: PMC10123994 DOI: 10.1186/s12920-023-01514-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/09/2023] [Indexed: 04/26/2023] Open
Abstract
Neurofibromatosis type 1 (NF1) presents an autosomal dominant, haploinsufficient, and multisystemic disorder with patches of skin café-au-lait spots, lisch nodules in the iris, even tumors in the peripheral nervous system or fibromatous skin. In this study, a Chinese young woman who suffered from NF1 disease with first-trimester spontaneous abortion was recruited. Analysis for whole exome sequencing (WES), Sanger sequencing, short tandem repeat (STR), and co-segregation was carried out. As results, a novel, heterozygous, de novo pathogenic variant (c.4963delA:p.Thr1656Glnfs*42) of the NF1 gene in the proband was identified. This pathogenic variant of the NF1 gene produced a truncated protein that lost more than one-third of the NF1 protein at the C-terminus including half of the CRAL-TRIO lipid-binding domain and nuclear localization signal (NLS), thus leading to pathogenicity (ACMG criteria: PVS1 + PM2 + PM2). Analysis for NF1 conservation in species revealed high conservation in different species. Analysis of NF1 mRNA levels in different human tissues showed low tissue specificity, which may affect multiple organs presenting other symptoms or phenotypes. Moreover, prenatal NF1 gene diagnosis showed both alleles as wild types. Thus, this NF1 novel variant probably underlays the NF1 pathogenesis in this pedigree, which would help for the diagnosis, genetic counseling, and clinical management of this disorder.
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Affiliation(s)
- Lisha Yang
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China
- Department of Obstetrics, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China
| | - Jingliang Cheng
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China
| | - Baixu Zhou
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China
- Department of Gynecology and Obstetrics, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Maomei Chen
- Department of Obstetrics, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Songyot Anuchapreeda
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Research Center of Pharmaceutical Nanotechnology, Chiang Mai University, Chiang Mai, 50200, Thailand.
| | - Junjiang Fu
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China.
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12
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Dunn T, Blaauw D, Das R, Narayanasamy S. nPoRe: n-polymer realigner for improved pileup-based variant calling. BMC Bioinformatics 2023; 24:98. [PMID: 36927439 PMCID: PMC10022090 DOI: 10.1186/s12859-023-05193-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/19/2023] [Indexed: 03/18/2023] Open
Abstract
Despite recent improvements in nanopore basecalling accuracy, germline variant calling of small insertions and deletions (INDELs) remains poor. Although precision and recall for single nucleotide polymorphisms (SNPs) now exceeds 99.5%, INDEL recall remains below 80% for standard R9.4.1 flow cells. We show that read phasing and realignment can recover a significant portion of false negative INDELs. In particular, we extend Needleman-Wunsch affine gap alignment by introducing new gap penalties for more accurately aligning repeated n-polymer sequences such as homopolymers ([Formula: see text]) and tandem repeats ([Formula: see text]). At the same precision, haplotype phasing improves INDEL recall from 63.76 to [Formula: see text] and nPoRe realignment improves it further to [Formula: see text].
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Affiliation(s)
- Tim Dunn
- University of Michigan, Ann Arbor, USA.
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13
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Dai X, Zhu Q, Wang C, Rukeye A, Cao Z, Shan T, Wang Y, Zhang J. F ST estimates of 94 populations in China based on STR markers. Forensic Sci Int Genet 2023; 64:102854. [PMID: 36893618 DOI: 10.1016/j.fsigen.2023.102854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/14/2023] [Accepted: 03/02/2023] [Indexed: 03/06/2023]
Abstract
The proper assessment of DNA evidence in cases of personal identification is a recurring theme in forensics. It is common practice to evaluate the strength of DNA evidence using the likelihood ratio (LR). The accurate use of population allele frequencies is a crucial problem in LR calculation. Allele frequency differences among different populations could be estimated by the FST values. Thus, FST would also affect LR values by correcting the allele frequencies. In this study, Chinese population allele frequency data were selected from population reports published in Chinese and English journals. The population-specific FST values of each population, the overall FST values of each province, each region, and the whole country, and the locus-specific FST values of different loci were calculated. The LRs using different allele frequencies and different FST values were compared based on the combination of simulated genotypes. As a result, the FST values of 94 populations, 19 provinces, 7 regions, and the whole country were obtained. The LR was overestimated using allele frequencies of the combined population containing multiple populations rather than using allele frequencies of a population, and the LRs after FST correction were lower than those without correction. Conclusively, the correction in conjunction with corresponding FST values can make the LRs more accurate and reasonable.
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Affiliation(s)
- Xuan Dai
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Qiang Zhu
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Chu Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Aosiman Rukeye
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Ze Cao
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Tiantian Shan
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yufang Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Ji Zhang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China.
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14
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Liu Q, Han Y, Hou X, Zhao S, Wang D, Li S, Wang Y. Genetic polymorphism and forensic efficiency of 21 autosomal STR loci from Shandong Han population in Northern China. Ann Hum Biol 2023; 50:341-344. [PMID: 37431877 DOI: 10.1080/03014460.2023.2224057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
BACKGROUND Highly polymorphic autosomal STR loci are useful for understanding population structure better and for forensic application, however the non-CODIS STR loci in the Han population of Shandong, located in Northern China, are not well-characterised. AIM To investigate population genetic polymorphism and forensic efficiency of 21 autosomal STR loci from the Shandong Han population in Northern China and reveal the genetic relationships with other populations both at home and abroad. SUBJECTS AND METHODS In this study, population genetic data of 21 autosomal STR loci included in the Goldeneye DNA ID 22NC Kit that includes four CODIS loci and 17 non-CODIS loci were determined for 523 unrelated Han individuals in Shandong. RESULTS Significant deviations from Hardy-Weinberg equilibrium were not observed. A total of 233 alleles were detected with allele frequencies ranging from 0.0010 to 0.3728. The combined power of discrimination was 0.99999999999999999999999990011134, and the combined power of exclusion was 0.99999999788131. Furthermore, in an analysis of population differentiation Nei's standard genetic distance and multidimensional scaling analysis, which were conducted based on the overlapping 15 STR loci, revealed that the Shandong Han population was most closely related to populations in close geographic proximity. CONCLUSIONS This study demonstrated that the 21 autosomal STR loci included in the GoldeneyeTM DNA ID 22NC system are highly polymorphic and suitable for forensic identification and paternity testing in the Shandong Han population. Additionally, the present results enrich the population genetic database.
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Affiliation(s)
- Qi Liu
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, P. R. China
| | - Yawen Han
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, P. R. China
| | - Xiudi Hou
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, P. R. China
| | - Shuquan Zhao
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Dan Wang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, P. R. China
| | - Shuyue Li
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, P. R. China
- School of Basic Medical Science, Xinjiang Medical University, Urumqi, P. R. China
| | - Yequan Wang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, P. R. China
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15
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Xu H, Miao X, Chai C, Tang H, Hu J, Zhao Z, Luo W, Zhu K, Zhou W. Establishment and characterization of a new Chinese hepatocellular carcinoma cell line, Hep-X1. Hum Cell 2023; 36:434-445. [PMID: 36152230 DOI: 10.1007/s13577-022-00797-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/18/2022] [Indexed: 01/07/2023]
Abstract
Hepatocellular carcinoma (HCC) is a highly aggressive and heterogeneous disease. Cell lines are commonly employed as in vitro models for cell type studies. However, the success rate of HCC primary culture establishment is low. In this study, we successfully established a liver cancer cell line, Hep-X1. Primary culture and passage of surgically removed tissues were used to establish hepatoma cell lines. Morphological examination, short tandem repeat (STR) analysis, immunohistochemical staining, doubling time, karyotype analysis, plate tumor formation experiments, organoid culture, and in vivo tumor formation investigations in animals were used to identify the cell lines. A novel liver cancer cell line, Hep-X1, was established based on morphology, immunophenotype, cytogenetics, and STR analysis. The novel cell line can be a valuable model for studying primary liver cancer.
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Affiliation(s)
- Hao Xu
- The Forth Department of General Surgery, The First Hospital of Lanzhou University, No.1 Donggang West Road, Chengguan District, Lanzhou, 730000, Gansu, China.
| | - Xin Miao
- State Key Laboratory of Veterinary Etiological Biology & OIE/National Foot and Mouth Disease Reference Laboratory & Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, LanZhou, 730000, China
| | - Changpeng Chai
- The Forth Department of General Surgery, The First Hospital of Lanzhou University, No.1 Donggang West Road, Chengguan District, Lanzhou, 730000, Gansu, China
| | - Huan Tang
- The Forth Department of General Surgery, The First Hospital of Lanzhou University, No.1 Donggang West Road, Chengguan District, Lanzhou, 730000, Gansu, China
| | - Jinjing Hu
- The Forth Department of General Surgery, The First Hospital of Lanzhou University, No.1 Donggang West Road, Chengguan District, Lanzhou, 730000, Gansu, China
| | - Zhenjie Zhao
- The Forth Department of General Surgery, The First Hospital of Lanzhou University, No.1 Donggang West Road, Chengguan District, Lanzhou, 730000, Gansu, China
| | - Wei Luo
- The Forth Department of General Surgery, The First Hospital of Lanzhou University, No.1 Donggang West Road, Chengguan District, Lanzhou, 730000, Gansu, China
| | - Kexiang Zhu
- The Forth Department of General Surgery, The First Hospital of Lanzhou University, No.1 Donggang West Road, Chengguan District, Lanzhou, 730000, Gansu, China
| | - Wence Zhou
- Department of General Surgery, The Second Hospital of Lanzhou University, Lanzhou, 730000, China.
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730000, China.
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16
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Arabfard M, Salesi M, Nourian YH, Arabipour I, Maddi AA, Kavousi K, Ohadi M. Global abundance of short tandem repeats is non-random in rodents and primates. BMC Genom Data 2022; 23:77. [PMID: 36329409 DOI: 10.1186/s12863-022-01092-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Background While of predominant abundance across vertebrate genomes and significant biological implications, the relevance of short tandem repeats (STRs) (also known as microsatellites) to speciation remains largely elusive and attributed to random coincidence for the most part. Here we collected data on the whole-genome abundance of mono-, di-, and trinucleotide STRs in nine species, encompassing rodents and primates, including rat, mouse, olive baboon, gelada, macaque, gorilla, chimpanzee, bonobo, and human. The collected data were used to analyze hierarchical clustering of the STR abundances in the selected species. Results We found massive differential STR abundances between the rodent and primate orders. In addition, while numerous STRs had random abundance across the nine selected species, the global abundance conformed to three consistent < clusters>, as follows: <rat, mouse>, <gelada, macaque, olive baboon>, and <gorilla, chimpanzee, bonobo, human>, which coincided with the phylogenetic distances of the selected species (p < 4E-05). Exceptionally, in the trinucleotide STR compartment, human was significantly distant from all other species. Conclusion Based on hierarchical clustering, we propose that the global abundance of STRs is non-random in rodents and primates, and probably had a determining impact on the speciation of the two orders. We also propose the STRs and STR lengths, which predominantly conformed to the phylogeny of the selected species, exemplified by (t)10, (ct)6, and (taa4). Phylogenetic and experimental platforms are warranted to further examine the observed patterns and the biological mechanisms associated with those STRs.
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17
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Ohuchi T, Guan X, Hirai E, Hashiyada M, Manabe S, Akane A, Adachi N, Tamaki K, Funayama M. Allele frequencies of 31 autosomal short tandem repeat (auSTR) loci obtained using the Precision ID GlobalFiler™ NGS STR Panel v2 in 322 individuals from the Japanese population. Leg Med (Tokyo) 2022; 59:102151. [PMID: 36191412 DOI: 10.1016/j.legalmed.2022.102151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/18/2022] [Accepted: 09/22/2022] [Indexed: 10/31/2022]
Abstract
In human identification methods that target short tandem repeats (STRs), massively parallel sequencing (MPS) technology has made it possible to genotype at the level of the specific sequence itself. This allows for the detection of repeat unit variants and single nucleotide polymorphisms (SNPs) adjacent to the STRs. Using the GlobalFiler™ NGS STR Panel v2, Ion S5, and Converge software, this study constructed a Japanese database of 31 autosomal STRs (auSTRs) and two sex markers from 322 individuals. After excluding some sequence errors and stutters, a total of 31 novel alleles were identified. Additionally, using the allele frequencies of 31 auSTR loci, the match probabilities for the length-based and sequence-based data were calculated to be 1.433 × 10-34 and 9.163 × 10-38, respectively. These values are at least nine orders of magnitude higher than that obtained from 21 auSTR loci in the Japanese population using the conventional capillary electrophoresis method. The database generated in this study is expected to be implemented in forensic practice and used to solve difficult casework.
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Affiliation(s)
- Tsukasa Ohuchi
- Department of Forensic Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan.
| | - Xueting Guan
- Department of Forensic Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Eriko Hirai
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masaki Hashiyada
- Department of Legal Medicine, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010, Japan
| | - Sho Manabe
- Department of Legal Medicine, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010, Japan
| | - Atsushi Akane
- Department of Legal Medicine, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010, Japan
| | - Noboru Adachi
- Department of Legal Medicine, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898, Japan
| | - Keiji Tamaki
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masato Funayama
- Department of Forensic Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
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18
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Fang L, Liu Q, Monteys AM, Gonzalez-Alegre P, Davidson BL, Wang K. DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing. Genome Biol 2022; 23:108. [PMID: 35484600 PMCID: PMC9052667 DOI: 10.1186/s13059-022-02670-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/08/2022] [Indexed: 12/12/2022] Open
Abstract
Despite recent improvements in basecalling accuracy, nanopore sequencing still has higher error rates on short-tandem repeats (STRs). Instead of using basecalled reads, we developed DeepRepeat which converts ionic current signals into red-green-blue channels, thus transforming the repeat detection problem into an image recognition problem. DeepRepeat identifies and accurately quantifies telomeric repeats in the CHM13 cell line and achieves higher accuracy in quantifying repeats in long STRs than competing methods. We also evaluate DeepRepeat on genome-wide or candidate region datasets from seven different sources. In summary, DeepRepeat enables accurate quantification of long STRs and complements existing methods relying on basecalled reads.
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Affiliation(s)
- Li Fang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Qian Liu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,School of Life Sciences, College of Science, University of Nevada, Las Vegas, 4505 S Maryland Pkwy, Las Vegas, NV, 89154, USA. .,Nevada Institute of Personalized Medicine, College of Science, University of Nevada, Las Vegas, 4505 S Maryland Pkwy, Las Vegas, NV, 89154, USA.
| | - Alex Mas Monteys
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Pedro Gonzalez-Alegre
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Beverly L Davidson
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Yang J, Chen J, Ji Q, Li K, Deng C, Kong X, Xie S, Zhan W, Mao Z, Zhang B, Yu Y, Li D, Cao Y, Ye K, Liu Q, Wu M, Chen F, Chen P. Could routine forensic STR genotyping data leak personal phenotypic information? Forensic Sci Int 2022; 335:111311. [PMID: 35468577 DOI: 10.1016/j.forsciint.2022.111311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/19/2022] [Accepted: 04/13/2022] [Indexed: 11/22/2022]
Abstract
The application of forensic genetic markers must comply with privacy rights and legal policies on a premise that the markers do not expose phenotypic information. The most widely-used short tandem repeats (STRs) are generally viewed as 'junk' DNA because most STRs are located in non-coding regions and therefore refrain from leaking phenotypic traits. But with a deepening understanding of phenotypes and underlying genetic structure, whether STRs could potentially reflect any phenotypic information may need re-examining. Therefore, we performed the following analyses. First, we analyzed the association between 15 STRs and three facial characteristics (single or double eyelid, with or without epicanthus, unattached or attached earlobe) on 721 unrelated Han Chinese individuals. Then, we collected 27199 individuals' STRs and geographic data from the literature to investigate the association between STRs and bio-geographic information, and predict geographic information by STRs on additional 1993 unrelated individuals. We found that there was scarcely any association between STRs with studied facial characteristics. Although allele19 in D2S1338 and allele 18 in FGA (P = 0.0032, P = 0.0030, respectively after Bonferroni correction) showed statistical significance, the prediction effectiveness was very low. For the STRs and bio-geographic information, the principal component analysis showed the first three components could explain 87.7% of the variance, but the prediction accuracy only reached 25.2%. We demonstrated that the forensic phenotypes are usually complex traits, it is hardly possible to uncover phenotypic information by testing only dozens of STR loci.
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Steffen CR, Huszar TI, Borsuk LA, Vallone PM, Gettings KB. A multi-dimensional evaluation of the 'NIST 1032' sample set across four forensic Y-STR multiplexes. Forensic Sci Int Genet 2022; 57:102655. [PMID: 35007854 DOI: 10.1016/j.fsigen.2021.102655] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/09/2021] [Accepted: 12/12/2021] [Indexed: 02/08/2023]
Abstract
This manuscript reports Y-chromosomal short tandem repeat (Y-STR) haplotypes for 1032 male U.S. population samples across 30 Y-STR loci characterized by three capillary electrophoresis (CE) length-based kits (PowerPlex Y23 System, Yfiler Plus PCR Amplification Kit, and Investigator Argus Y-28 QS Kit) and one sequence-based kit (ForenSeq DNA Signature Prep Kit): DYF387S1, DYS19, DYS385 a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS505, DYS518, DYS522, DYS533, DYS549, DYS570, DYS576, DYS612, DYS627, DYS635, DYS643, and Y-GATA-H4. The length-based Y-STR haplotypes include six loci that are not reported in the sequence-based kit (DYS393, DYS449, DYS456, DYS458, DYS518, and DYS627), whereas three loci included in the sequence-based kit are not present in length-based kits (DYS505, DYS522, and DYS612). For the latter, a custom multiplex was used to generate CE length-based data, allowing 1032 samples to be evaluated for concordance across the 30 Y-STR loci included in these four commercial Y-STR typing kits. Discordances between typing methods were analyzed further to assess underlying causes such as primer binding site mutations and flanking region insertions/deletions. Allele-level frequency and statistical information is provided for sequenced loci, excluding the multi-copy loci DYF387S1 and DYS385 a/b, for which locus-specific haplotype-level frequencies are provided instead. The resulting data reveals the degree of information gained through sequencing: 88% of sequenced Y-STR loci contain additional sequence-based alleles compared to length-based data, with the DYS389II locus containing the most additional alleles (51) observed by sequencing. Despite these allelic increases, only minimal improvement was observed in haplotype resolution by sequence, with all four commercial kits providing a similar ability to differentiate length-based haplotypes in this sample set. Finally, a subset of 369 male samples were compared to their corresponding additionally sequenced father samples, revealing the sequence basis for the 50 length-based changes observed, and no additional sequence-based mutations. GenBank accession numbers are reported for each unique sequence, and associated records are available in the STRSeq Y-Chromosomal STR Loci National Center for Biotechnology Information (NCBI) BioProject, accession PRJNA380347. Haplotype data is updated in the Y-STR Haplotype Reference Database (YHRD) for the 'NIST 1032' data set to now achieve the level of maximal haplotype of YHRD. All supplementary files including revisions to previously published Y-STR data are available in the NIST Public Data Repository: U.S. population data for human identification markers, DOI 10.18434/t4/1500024.
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Khamse S, Arabfard M, Salesi M, Behmard E, Jafarian Z, Afshar H, Khazaei M, Ohadi M. Predominant monomorphism of the RIT2 and GPM6B exceptionally long GA blocks in human and enriched divergent alleles in the disease compartment. Genetica 2022; 150:27-40. [PMID: 34984576 DOI: 10.1007/s10709-021-00143-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/22/2021] [Indexed: 11/29/2022]
Abstract
Across human protein-coding genes, the human neuron-specific genes, RIT2 and GPM6B, contain the two longest GA short tandem repeats (STRs) of 11 and 9-repeats, respectively, the length ranges of which are functional, and result in gene expression alteration. Here we sequenced the RIT2 and GPM6B STRs in 600 human subjects, consisting of late-onset neurocognitive disorder (n = 200), multiple sclerosis (n = 200), and controls (n = 200). Furthermore, we selected two large human databases, including the general-population-based gnomAD ( https://gnomad.broadinstitute.org ) and a mainly disease-phenotype-archiving database, TOPMed ( https://www.nhlbiwgs.org ), to compare allele frequencies in the general populations vs. the disease compartment. The RIT2 and GPM6B GA-repeats were monomorphic in the human subjects studied, at lengths of 11 and 9-repeats, respectively, and were predominantly human-specific in formula. Exception included a 9/11 genotype of the RIT2 GA-STR in an isolate case of female multiple sclerosis. Exceedingly rare alleles of the two GA repeats were significantly enriched in TOPMed vs. the gnomAD. We report prime instances of predominant monomorphism for specific lengths of STRs in human, and possible enrichment of rare divergent alleles in the disease phenotype compartment. While STRs are most attended because of their high polymorphic nature, STR monomorphism is an underappreciated feature, which may have a link with natural selection and disease.
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Affiliation(s)
- S Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Arabfard
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - M Salesi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - E Behmard
- School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Z Jafarian
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - H Afshar
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Khazaei
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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Nishi T, Fukui K, Matumoto S, Takasu S, Iwadate K. Polymorphism and haplotype analysis of three novel short tandem repeat loci in the p11.4 region of human X chromosome. Int J Legal Med 2021. [PMID: 34741211 DOI: 10.1007/s00414-021-02739-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/26/2021] [Indexed: 10/19/2022]
Abstract
X-chromosomal short tandem repeats (X-STRs) are useful for the identification of absent single parents and complex blood relations. In the present study, we aimed to identify novel STR loci for use as DNA markers by conducting polymorphism and haplotype analyses. We detected three novel STR loci (LC552061, LC552062, and LC552063, with repetitive structures of (GGAA)n(GGGA)m, (CCTT)n(CCCT)m, and (ATTT)n, respectively) in the p11.4 region of the X chromosome. For these X-STRs, the polymorphism information content values ranged from 0.5766 to 0.6377 and the power of discrimination in males and females ranged from 0.6269 to 0.6844 and from 0.8105 to 0.8537, respectively. The linkage disequilibrium analysis revealed p values of < 0.0001, < 0.0001, and 0.00909 between LC552061 and LC552062, LC552061 and LC552063, and LC552062 and LC552063, respectively. Additional linkage disequilibrium analysis including seven previously analyzed loci (LC149476, LC149479, LC149480, LC149484, LC317283, LC317284, and LC317285) revealed a p value of < 0.001 among each of the five loci (LC149476, LC149479, LC149480, LC149484, and LC317283) and between LC317284 and LC317285, indicating that they were a linked group. These results indicate that, in addition to the seven previously detected loci, the three novel X-STR loci identified in the present study might be useful DNA markers for complex kinship analysis and might support the Investigator® Argus X-12 kit.
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Haddish K, Chierto E, Di Vella G, Lacerenza D, Raddi S, Aneli S, Bogale AL, Kidane E, Yizengaw A, Getaneh Y, Tewelemedhin G, Kumar HRS, Robino C. A reference database of forensic autosomal and gonosomal STR markers in the Tigray population of Ethiopia. Forensic Sci Int Genet 2021; 56:102618. [PMID: 34735940 DOI: 10.1016/j.fsigen.2021.102618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/31/2021] [Accepted: 10/20/2021] [Indexed: 11/20/2022]
Abstract
Allele frequencies of 21 autosomal STR markers (AmpF/STR GlobalFiler) and haplotype frequencies of 27 Y- and 12 X-STR markers (AmpF/STR YFiler Plus and Investigator Argus X-12, respectively) were investigated in the Tigray population of Ethiopia, representing the main population group in the Tigray regional state of Ethiopia and neighboring Eritrea. For autosomal STR allele frequencies, the average random match probability in the Tigray sample was 2.1 × 10-27. The average locus by locus FST distance calculated comparing autosomal STR allele frequencies from Tigray and from a broad regional reference dataset currently available for the Horn of Africa was 0.003. The Tigray male sample displayed high Y-STR diversity, with complete individualization of haplotypes using the AmpF/STR YFiler Plus panel. Analysis of molecular variance did not detect significant heterogeneity between Y-STR haplotypes observed in the present study and those previously reported in the literature for other Tigray population samples from Ethiopia and Eritrea. Study of the X-STR landscape in Tigray evidenced several distinctive features including: the molecular characterization of a novel null allele at locus DXS10146 with frequency > 1%; allele dependency between loci within linkage groups I and III; significant differences in haplotype distribution compared to other Horn of Africa populations, that should be taken into account in kinship analysis. The collected data can be used as a reference STR database by local forensic genetics services and in genetic identification procedures of victims of human trafficking in the Mediterranean Sea, which frequently involve individuals originating from the Horn of Africa.
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Herzig M, Maksimov P, Staubach C, Romig T, Knapp J, Gottstein B, Conraths FJ. Red foxes harbor two genetically distinct, spatially separated Echinococcus multilocularis clusters in Brandenburg, Germany. Parasit Vectors 2021; 14:535. [PMID: 34649615 PMCID: PMC8518320 DOI: 10.1186/s13071-021-05038-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 09/24/2021] [Indexed: 12/28/2022] Open
Abstract
Background Alveolar echinococcosis (AE) is a clinically serious zoonosis caused by the fox tapeworm Echinococcus multilocularis. We studied the diversity and the distribution of genotypes of E. multilocularis isolated from foxes in Brandenburg, Germany, and in comparison to a hunting ground in North Rhine-Westphalia. Methods Echinococcus multilocularis specimens from 101 foxes, 91 derived from Brandenburg and 10 derived from North Rhine-Westphalia, were examined. To detect potential mixed infections with different genotypes of E. multilocularis, five worms per fox were analyzed. For genotyping, three mitochondrial markers, namely cytochrome c oxidase subunit 1 (Cox1), NADH dehydrogenase subunit 1 (Nad1), and ATP synthase subunit 6 (ATP6), and the nuclear microsatellite marker EmsB were used. To identify nucleotide polymorphisms, the mitochondrial markers were sequenced and the data were compared, including with published sequences from other regions. EmsB fragment length profiles were determined and confirmed by Kohonen network analysis and grouping of Sammon’s nonlinear mapping with k-means clustering. The spatial distribution of genotypes was analyzed by SaTScan for the EmsB profiles found in Brandenburg. Results With both the mitochondrial makers and the EmsB microsatellite fragment length profile analyses, mixed infections with different E. multilocularis genotypes were detected in foxes from Brandenburg and North Rhine-Westphalia. Genotyping using the mitochondrial markers showed that the examined parasite specimens belong to the European haplotype of E. multilocularis, but a detailed spatial analysis was not possible due to the limited heterogeneity of these markers in the parasite population. Four (D, E, G, and H) out of the five EmsB profiles described in Europe so far were detected in the samples from Brandenburg and North Rhine-Westphalia. The EmsB profile G was the most common. A spatial cluster of the E. multilocularis genotype with the EmsB profile G was found in northeastern Brandenburg, and a cluster of profile D was found in southern parts of this state. Conclusions Genotyping of E. multilocularis showed that individual foxes may harbor different genotypes of the parasite. EmsB profiles allowed the identification of spatial clusters, which may help in understanding the distribution and spread of the infection in wildlife, and in relatively small endemic areas. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-05038-0.
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Affiliation(s)
- Mandy Herzig
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Pavlo Maksimov
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Christoph Staubach
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Thomas Romig
- Universität Hohenheim, Institut Für Biologie, Fachgebiet Parasitologie, Emil-Wolff-Straße 34, 70599, Stuttgart, Germany
| | - Jenny Knapp
- UMR CNRS 6249 Laboratoire Chrono-Environnement, Université Bourgogne Franche-Comté, 16 Route de Gray, 25030, Besançon, France.,Department of Parasitology-Mycology, National Reference Centre for Echinococcoses, University Hospital of Besançon, 25030, Besançon, France
| | - Bruno Gottstein
- Institute for Infectious Diseases, Faculty of Medicine, University of Berne, 3001, Berne, Switzerland
| | - Franz J Conraths
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
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Yang J, Yan Z, Liu Y, Zhu X, Li R, Liu P, Yan L, Qiao J, Zhi X. Application of next-generation sequencing to preimplantation genetic testing for recurrent hydatidiform mole patients. J Assist Reprod Genet 2021; 38:2881-2891. [PMID: 34608573 DOI: 10.1007/s10815-021-02325-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 09/20/2021] [Indexed: 11/26/2022] Open
Abstract
PURPOSE To study the application of next-generation sequencing on preimplantation genetic testing for recurrent hydatidiform mole patients. METHODS A total of ten recurrent hydatidiform mole patients aged 27-34 years with a history of at least twice hydatidiform moles and no normal pregnancy were collected from 2019 to 2020. The diagnosis of hydatidiform mole type was clarified using short tandem repeat genotyping on products of conception, and whole-exome sequencing was applied for all patients and their partners. Seven recurrent hydatidiform mole patients with complete hydatidiform mole/partial hydatidiform mole type among previous hydatidiform mole tissues and no Pathogenetic/Likely pathogenetic/Uncertain significance variants in NLRP7/KHDC3L/MEI1/C11orf80 underwent a procedure of preimplantation genetic testing. Next-generation sequencing for analyzing the copy number variants and the numbers of heterozygous single nucleotide polymorphism was adopted to clarify the ploidy and parental origin of the embryo chromosomes in vitro. Embryos with biparental diploidy were selected for transfer. RESULTS Seven patients have undergone the procedure of preimplantation genetic testing, and twenty-three embryos were obtained, among which 82.6% (n = 19) were identified transferrable and 17.4% (n = 4) were identified aneuploid. Two patients have delivered healthy babies and another is currently in the second trimester after transfer. CONCLUSION Analyzing the copy number variants and the numbers of heterozygous single nucleotide polymorphism on the basis of next-generation sequencing can be utilized in the procedure of preimplantation genetic testing among part of recurrent hydatidiform mole patients. The current study is effective to reduce the occurrence of hydatidiform mole with improved clinical strategy, the advanced testing technology and analysis methods, as three of seven patients have conceived or delivered successfully.
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Affiliation(s)
- Jingyi Yang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
| | - Zhiqiang Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
| | - Yan Liu
- Department of Pathology, School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing, 100191, China
| | - Xiaohui Zhu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
| | - Rong Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
| | - Ping Liu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
| | - Liying Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
| | - Xu Zhi
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China.
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Manabe S, Fukagawa T, Fujii K, Mizuno N, Sekiguchi K, Akane A, Tamaki K. Development and validation of Kongoh ver. 3.0.1: Open-source software for DNA mixture interpretation in the GlobalFiler system based on a quantitative continuous model. Leg Med (Tokyo) 2021; 54:101972. [PMID: 34629243 DOI: 10.1016/j.legalmed.2021.101972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/27/2021] [Accepted: 09/28/2021] [Indexed: 10/20/2022]
Abstract
Probabilistic genotyping software based on continuous models is effective for interpreting DNA profiles derived from DNA mixtures and small DNA samples. In this study, we updated our previously developed Kongoh software (to ver. 3.0.1) to interpret DNA profiles typed using the GlobalFiler™ PCR Amplification Kit. Recently, highly sensitive typing systems such as the GlobalFiler system have facilitated the detection of forward, double-back, and minus 2-nt stutters; therefore, we implemented statistical models for these stutters in Kongoh. In addition, we validated the new version of Kongoh using 2-4-person mixtures and DNA profiles with degradation in the GlobalFiler system. The likelihood ratios (LRs) for true contributors and non-contributors were well separated as the information increased (i.e., larger peak height and fewer contributors), and these LRs tended to neutrality as the information decreased. These trends were observed even in profiles with DNA degradation. The LR values were highly reproducible, and the accuracy of the calculation was also confirmed. Therefore, Kongoh ver. 3.0.1 is useful for interpreting DNA mixtures and degraded DNA samples in the GlobalFiler system.
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Affiliation(s)
- Sho Manabe
- Department of Legal Medicine, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010, Japan.
| | - Takashi Fukagawa
- Fourth Biological Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Koji Fujii
- Fourth Biological Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Natsuko Mizuno
- Fourth Biological Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Kazumasa Sekiguchi
- Fourth Biological Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Atsushi Akane
- Department of Legal Medicine, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010, Japan
| | - Keiji Tamaki
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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Huang Y, Liu C, Xiao C, Chen X, Han X, Yi S, Huang D. Mutation analysis of 28 autosomal short tandem repeats in the Chinese Han population. Mol Biol Rep 2021; 48:5363-5369. [PMID: 34213710 DOI: 10.1007/s11033-021-06522-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 06/25/2021] [Indexed: 11/26/2022]
Abstract
Short tandem repeats (STRs) have been extensively used in forensic genetics. However, according to previous studies, the mutation rates of STRs are relatively high and are affected by many factors. Therefore, it is important to analyze STR mutations and determine the influence of underlying factors on STR mutation rates. Mutation rates of 28 autosomal STRs were determined from 8708 paternity testing cases in the Chinese Han population, and the relationships between STR mutation rates and population, sex, age, allele length and heterozygosity were investigated. A total of 279 mutations were observed at 27 loci in a total of 233,530 meiosis cases, including 273 (97.8%) one-step, 5 (1.8%) two-step and 1 (0.4%) three-step mutations. The overall average mutation rate was 1.19 × 10-3 (95% CI 1.06 × 10-3 - 1.34 × 10-3) ranging from 0 (TPOX) to 2.79 × 10-3 (D13S325). Mutation rate comparisons revealed statistically significant differences at several STRs among populations. Paternal mutations occurred more frequently than maternal mutations, at a ratio of 6.04:1, and the mutation rate tended to increase with paternal age. Moreover, our study revealed a bias towards contraction mutations for long alleles and expansion mutations for short alleles. No obvious bias was observed in the overall mutation direction. In addition, STR loci with higher expected heterozygosity (Hexp) tended to have higher mutation rates. This work revealed the relationships between STR mutation rates and several influencing factors, providing useful data and information for further research on STR mutations in forensic genetics.
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Affiliation(s)
- Yujie Huang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cong Liu
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chao Xiao
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoying Chen
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xueli Han
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shaohua Yi
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Daixin Huang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Taira Y, Shimoji Y, Nakasone T, Arakaki Y, Nakamoto T, Kinjo T, Kudaka W, Mekaru K, Aoki Y. A high-risk gestational trophoblastic neoplasia derived from a complete hydatidiform mole with coexisting fetus identified by short tandem repeats analysis: A case report. Case Rep Womens Health 2021; 31:e00336. [PMID: 34195021 PMCID: PMC8233190 DOI: 10.1016/j.crwh.2021.e00336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 11/30/2022] Open
Abstract
A complete hydatidiform mole coexisting with a fetus (CHMCF) is a rare form of twin pregnancy. High-risk gestational trophoblastic neoplasia (GTN) can occur after a CHMCF pregnancy, although the frequency is low. In cases of GTN, the clinical diagnosis and that based on the International Federation of Gynecology and Obstetrics (FIGO) scoring system can differ. This case report concerns a patient with a choriocarcinoma that was initially diagnosed and treated as a low-risk stage III GTN following a live birth from a CHMCF pregnancy. We used short tandem repeat (STR) analysis to identify the causative pregnancy as the patient's earlier complete hydatidiform mole. Clinicians should anticipate a high-risk GTN when treating persistent trophoblastic disease (PTD) in patients with a non-typical course. A fetus and a complete hydatidiform mole can coexist as a twin pregnancy. A complete hydatidiform mole coexisting with a fetus can rarely cause choriocarcinoma. Short tandem repeat analysis can be used to identify causative pregnancies. Causative pregnancy is a risk factor for persistent trophoblastic disease.
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Manabe S, Fujii K, Fukagawa T, Mizuno N, Sekiguchi K, Inoue K, Hashiyada M, Akane A, Tamaki K. Evaluation of probability distribution models for stutter ratios in the typing system of GlobalFiler and 3500xL Genetic Analyzer. Leg Med (Tokyo) 2021; 52:101906. [PMID: 34015722 DOI: 10.1016/j.legalmed.2021.101906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/06/2021] [Accepted: 05/07/2021] [Indexed: 11/19/2022]
Abstract
As DNA typing systems have become increasingly sensitive in recent years, probability distribution models for back, forward, double-back, and minus 2-nt stutter ratios have been desired to be considered in DNA evidence interpretation using specific software programs. However, experimental investigations have been insufficient, especially for forward, double-back, and minus 2-nt stutters. In this study, we experimentally reevaluated the probability distribution models for each stutter ratio in the typing systems of GlobalFiler™ PCR Amplification Kit and 3500xL Genetic Analyzer from Thermo Fisher Scientific. In addition, to enhance the reliability of longest uninterrupted stretch (LUS) values and corrected allele numbers used in previously developed models for stutter ratios using sequence information (i.e., LUS model and multi-seq model), we propose the weighted average of LUS values and corrected allele numbers based on the number of observations in sequence-based population data. Back stutter ratios demonstrated a positive correlation with allele numbers (allele model) in eight loci, LUS values (LUS model) in eight loci, and corrected allele numbers (multi-seq model) in five loci. The forward stutter ratios (FSRs) of D22S1045 followed the LUS model. FSRs other than D22S1045 and double-back stutter ratios followed the LUS model by considering multiple loci together. Minus 2-nt stutter ratios observed in SE33 and D1S1656 did not increase with the increase in the allele numbers. The adopted models for each stutter ratio can be implemented in software programs for DNA evidence interpretation and enable a reliable interpretation of crime stain profiles in forensic caseworks.
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Affiliation(s)
- Sho Manabe
- Department of Legal Medicine, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010, Japan.
| | - Koji Fujii
- Fourth Biological Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Takashi Fukagawa
- Fourth Biological Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Natsuko Mizuno
- Fourth Biological Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Kazumasa Sekiguchi
- Fourth Biological Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Kana Inoue
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masaki Hashiyada
- Department of Legal Medicine, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010, Japan
| | - Atsushi Akane
- Department of Legal Medicine, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010, Japan
| | - Keiji Tamaki
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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Desnos-Ollivier M, Fekkar A, Bretagne S. Earliest case of Candida auris infection imported in 2007 in Europe from India prior to the 2009 description in Japan. J Mycol Med 2021; 31:101139. [PMID: 33965885 DOI: 10.1016/j.mycmed.2021.101139] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/04/2021] [Accepted: 04/05/2021] [Indexed: 11/20/2022]
Abstract
Candida auris is an emerging pathogen frequently associated with multidrug resistance and involved in many worldwide outbreaks. We here report the first European imported case in France due to isolate belonging of the South Indian clade I and the importance of prevention measure to avoid fungal spreading.
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31
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Corrêa H, Cortellini V, Franceschetti L, Verzeletti A. Large fragment demineralization: an alternative pretreatment for forensic DNA typing of bones. Int J Legal Med 2021; 135:1417-24. [PMID: 33587178 DOI: 10.1007/s00414-021-02531-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 02/03/2021] [Indexed: 10/22/2022]
Abstract
In forensic genetics, the analysis of postmortem bones is one of the most challenging due to the low quantity of degraded endogenous DNA. The most widely used approach for sample preparation, in those cases, is pulverizing the bone. However, processing pulverized bone is extremely delicate, requiring strict laboratory conditions and operating procedures. In fact, several recent publications have focused on non-powder approaches. The objectives of this study were, thus, to validate a non-powder protocol for DNA extraction from forensic bones and an alternative pretreatment, large fragment demineralization (LFD). Thirty human femurs and tibiae received by the Legal Medicine Institute of Brescia, Italy, were included in the study. Bone powder and one transversal section of the diaphysis were sampled from each bone. DNA extraction from the powder was carried out using PrepFiler BTA (BTA), while the transversal section was submitted to the alternative demineralizing pretreatment (LFD) followed by DNA extraction using the QIAamp DNA Investigator. DNA extracts were assessed for human DNA quantity and degradation by means of a validated in-house qPCR assay and amplified with commercial kits. Inhibition assessment was carried out through Quality Sensor analysis using 24plex QS Kit. The differences in quantity, quality of human DNA, and number of alleles detected between both methods were comparable and not statistically significant. We propose the use of the LFD protocol as a complementary approach capable of confirming the genotypes or detect alleles not observed using BTA, without the need for pulverization.
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Young B, Marciano M, Crenshaw K, Duncan G, Armogida L, McCord B. Match statistics for sequence-based alleles in profiles from forensic PCR-mps kits. Electrophoresis 2021; 42:756-765. [PMID: 33314164 DOI: 10.1002/elps.202000087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 11/09/2020] [Accepted: 11/29/2020] [Indexed: 11/08/2022]
Abstract
The first autosomal sequence-based allele (aka SNP-STR haplotype) frequency database for forensic massively parallel sequencing (MPS) has been published, thereby removing one of the remaining barriers to implementing MPS in casework. The database was developed using a specific set of flank trim sites. If different trim sites or different kits with different primers are used for casework, then SNP-STR haplotypes may be detected that do not have frequencies in the database. We describe a procedure to address calculation of match probabilities when casework samples are generated using an MPS kit with different trim sites than those present in the relevant population frequency database. The procedure provides a framework for comparison of any MPS kit or database combination while also accommodating comparison of MPS and CE profiles.
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Affiliation(s)
| | - Michael Marciano
- Forensic & National Security Sciences Institute, Syracuse University, Syracuse, NY, USA
| | - Karin Crenshaw
- Broward County Sheriff's Office, Fort Lauderdale, FL, USA
| | - George Duncan
- Nova Southeastern University, Fort Lauderdale, FL, USA
| | | | - Bruce McCord
- Florida International University, Miami, FL, USA
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Abstract
Short tandem repeats (STRs) are widely used as DNA markers in paternity testing and criminal investigations because of their high genetic polymorphism among individuals in population. However, many factors influence genetic variations of STRs. Therefore, understanding STR information within individual populations could provide database and scientifically reliable STR genotyping for forensic genetic purposes. We aimed to examine allele frequencies of X-STRs, including some forensic parameters, in a northern Thai population. A retrospective descriptive study was conducted by collecting X-STR data from unrelated individuals living in a northern region of Thailand. The allele frequency and forensic parameters - for example polymorphism information content (PIC), power of discrimination in females and males (PDf and PDm), mean exclusion chance (MEC) and haplotype frequency - were calculated. The Hardy-Weinberg equilibrium was analysed. A total of 132 alleles were observed, with corresponding allele frequency ranging from 0.0064 to 0.4904. The PIC of all loci was >0.6, representing high genetic polymorphism, except DXS8378 and DXS7423. Notably, DXS10135 was the most diverse loci with the highest PD and MEC, while DXS7423 was the least polymorphic marker with the lowest PD and MEC. The highest haplotype diversity in male data was on linkage group III (DXS10101-DXS10103-HPRTB) by 0.9895. The genetic distance analysis demonstrated that the northern Thai population had a close relationship with Taiwanese (DA = 0.023). There are no significant deviations among the Hardy-Weinberg equilibrium except DXS10148. This study has established a northern Thai X-STRs reference database to be used as a tool for forensic genetic purposes.
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Affiliation(s)
- Supakit Khacha-Ananda
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Thailand
| | - Phatcharin Mahawong
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Thailand
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Chen QF, Kang KL, Song JJ, Zhang C, Yu ZL, Zhao GB, Wu H, Ji AQ, Ye J, Wang L. Allelic diversity and forensic estimations of the Beijing Hans: Comparative data on sequence-based and length-based STRs. Forensic Sci Int Genet 2021; 51:102424. [PMID: 33248347 DOI: 10.1016/j.fsigen.2020.102424] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 10/25/2020] [Accepted: 11/01/2020] [Indexed: 11/24/2022]
Abstract
Short tandem repeat (STR) profiling is routinely used in forensic genetics. At present, STR analysis is mainly performed by capillary electrophoresis (CE). However, due to limitations associated with the CE method, STR genotyping has been limited to length polymorphisms only. Because next generation sequencing (NGS) is capable of providing full resolution STR data at the sequence variation level, the individual identification capability of forensic STR loci could be significantly improved. Here we present sequence-based STR data for the Beijing Han population in which 291 individuals were screened for 23 commonly used forensic STRs using the SeqTypeR24 CASE kit on an Ion PGM platform. In total, 234 length-based alleles and 356 sequence-based alleles, which included 22 novel core repeat sequences, were observed. The sequence-based matching probability and power of discrimination were superior to the length-based numbers for 16 loci bearing micro-variant alleles. Combined matching probability reached 8.2 × 10-29 for 23 STR loci at the sequence level. This was two orders of magnitude higher than the parameters at length level and provides a data base for sequence-based STR casework applications.
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Joy L, Paulose S, Divya PR, Ravi C, Basheer VS, Kumar R, Singh RK, Mohindra V, Lal KK. Microsatellite marker development in Spanish mackerel Scomberomorus commerson using third generation sequencing technology. Mol Biol Rep 2020; 47:10005-10014. [PMID: 33170425 DOI: 10.1007/s11033-020-05975-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/03/2020] [Indexed: 11/28/2022]
Abstract
Spanish mackerel S. commerson belonging to family Scombridae, represent a group of highly commercial marine fisheries with an ever-growing demand world over. Analysing the genetic diversity of this species is of utmost importance and necessary for conservation purposes. Microsatellites are molecular tools with advantages that are ideal for population analyses. This study provides the first multiplex panel set of species-specific microsatellite loci for S. commerson that can be applied when assessing both intra- and inter population genetic variation. Microsatellite marker panels were developed in S. commerson, using Third Generation Sequencing technology in PacBio RSII, based on Single-Molecule Real-Time (SMRT). Thirty- two microsatellite loci were isolated and characterized for S. commerson, by genotyping 20 individuals each obtained from the Kochi and Veraval in the Arabian sea and Chennai along Bay of Bengal coast (n = 3). The number of alleles per locus in S. commerson varied from 4 to 17, while the mean observed and expected heterozygosities ranged from 0.656 to 0.753. The Polymorphic Information Content (PIC) were highly informative, 85% loci with PIC value 0 > 0.75. This suite of markers provides the first species specific nuclear multiplex microsatellite marker panels (32 loci) for S. commerson and thus allows assessment of different populations structures of the species across its distribution range, with more specificity. These newly developed loci have also been validated for cross transferability in another scomberid fish Scomberomorus guttatus.
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Affiliation(s)
- Linu Joy
- PMFGR Centre, ICAR NBFGR, Kochi, India
| | | | - P R Divya
- PMFGR Centre, ICAR NBFGR, Kochi, India.
| | | | | | - Rajesh Kumar
- ICAR National Bureau of Fish Genetic Resources, Lucknow, India
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Zhabagin M, Sabitov Z, Tarlykov P, Tazhigulova I, Junissova Z, Yerezhepov D, Akilzhanov R, Zholdybayeva E, Wei LH, Akilzhanova A, Balanovsky O, Balanovska E. The medieval Mongolian roots of Y-chromosomal lineages from South Kazakhstan. BMC Genet 2020; 21:87. [PMID: 33092538 PMCID: PMC7583311 DOI: 10.1186/s12863-020-00897-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 08/05/2020] [Indexed: 12/02/2022] Open
Abstract
Background The majority of the Kazakhs from South Kazakhstan belongs to the 12 clans of the Senior Zhuz. According to traditional genealogy, nine of these clans have a common ancestor and constitute the Uissun tribe. There are three main hypotheses of the clans’ origin, namely, origin from early Wusuns, from Niru’un Mongols, or from Darligin Mongols. We genotyped 490 samples of South Kazakhs by 35 Y-chromosomal SNPs (single nucleotide polymorphism) and 17 STRs (short tandem repeat). Additionally, 133 samples from citizen science projects were included into the study. Results We found that three Uissun clans have unique Y-chromosomal profiles, but the remaining six Uissun clans and one non-Uissun clan share a common paternal gene pool. They share a high frequency (> 40%) of the C2*-ST haplogroup (marked by the SNP F3796), which is associated with the early Niru’un Mongols. Phylogenetic analysis of this haplogroup carried out on 743 individuals from 25 populations of Eurasia has revealed a set of haplotype clusters, three of which contain the Uissun haplotypes. The demographic expansion of these clusters dates back to the 13-fourteenth century, coinciding with the time of the Uissun’s ancestor Maiky-biy known from historical sources. In addition, it coincides with the expansion period of the Mongol Empire in the Late Middle Ages. A comparison of the results with published aDNA (ancient deoxyribonucleic acid) data and modern Y haplogroups frequencies suggest an origin of Uissuns from Niru’un Mongols rather than from Wusuns or Darligin Mongols. Conclusions The Y-chromosomal variation in South Kazakh clans indicates their common origin in 13th–14th centuries AD, in agreement with the traditional genealogy. Though genetically there were at least three ancestral lineages instead of the traditional single ancestor. The majority of the Y-chromosomal lineages of South Kazakhstan was brought by the migration of the population related to the medieval Niru’un Mongols.
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Affiliation(s)
- Maxat Zhabagin
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan. .,National Center for Biotechnology, Nur-Sultan, Kazakhstan.
| | - Zhaxylyk Sabitov
- L.N. Gumilyov Eurasian National University, Nur-Sultan, Kazakhstan.,Young Researchers Alliance, Nur-Sultan, Republic of Kazakhstan
| | - Pavel Tarlykov
- National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Inkar Tazhigulova
- Forensic Science Center of the Ministry of Justice of the Republic of Kazakhstan, Nur-Sultan, Kazakhstan
| | - Zukhra Junissova
- Research Institute of Archeology named after K.A. Akishev, Nur-Sultan, Republic of Kazakhstan
| | - Dauren Yerezhepov
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | | | | | - Lan-Hai Wei
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China.,Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Ainur Akilzhanova
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Oleg Balanovsky
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia.,Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia
| | - Elena Balanovska
- Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia
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Puthenpura V, Gueye-Ndiaye S, Joshi S, Puvabanditsin S, Carayannopoulos MO. Social and legal implications of urine drug screen analysis in the neonate: A case of suspected specimen mishandling. Clin Chim Acta 2020; 511:104-106. [PMID: 33002470 DOI: 10.1016/j.cca.2020.09.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 09/19/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND The legal implications associated with illicit drug use during pregnancy are significant, as providers are required to notify child protective services when a drug-exposed infant is identified. CASE REPORT The case presented involves possible specimen mishandling in two infants at risk for in utero drug exposure and describes alternative methodologies available to confirm specimen identity. CONCLUSIONS It is critical that institutions establish and adhere to stringent procedures when screening newborns.
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Affiliation(s)
- Vidya Puthenpura
- Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Seyni Gueye-Ndiaye
- Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Sonali Joshi
- Robert Wood Johnson University Hospital, New Brunswick, NJ, United States
| | - Surasak Puvabanditsin
- Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, United States
| | - Mary O Carayannopoulos
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, United States.
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38
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Liu Y, Zheng XZ, Wang YX, Sun XJ, Li Y, Liu CR. [Molecular pathological diagnosis of twin pregnancy with complicated genetical characteristics]. Zhonghua Bing Li Xue Za Zhi 2020; 49:788-93. [PMID: 32746544 DOI: 10.3760/cma.j.cn112151-20200106-00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the molecular pathological diagnostic strategy of twin pregnancy(TP) with complex genetic characteristics, using p57 immunohistochemistry and short tandem repeat (STR) genotyping. Methods: Ten cases of TP with suspected hydatidiform mole(HM) according to pathological morphology were collected in Peking University Third Hospital from 2015 to 2019, and were subject to p57 immunohistochemistry, STR genotyping and follow-up. Results: The age of ten patients ranged 23 to 36 years, with an average of 29.5 years. Seven patients accepted assisted reproductive techniques in this conception. Three patients with "divergent" p57 staining pattern were diagnosed as TP with complete HM by STR, in which one had a persistent trophoblastic disease. The villi of five patients were consistently positive for p57, but the genotyping result was polyploid and suspicious as TP. Four of them showed excessive paternal alleles at more than 40% of the loci, suggesting that concomitant partial moles could not be excluded. One patient was diagnosed as TP without HM according to the maternal allelic predominance at all loci in villi. Two patients with p57 "divergent" and "discordant" staining villi were genotyped as TP with mosaic conception. Conclusions: The correct identification of p57 staining pattern and accurate interpretation of STR genotyping results are important in diagnosing TP. It may assist pathologists in making a definite or likely diagnosis of TP with complex genetic features to fulfill clinical triage strategies and contribute to formulate a reasonable follow-up approach.
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Afshar H, Adelirad F, Kowsari A, Kalhor N, Delbari A, Najafipour R, Foroughan M, Bozorgmehr A, Khamse S, Nazaripanah N, Ohadi M. Natural Selection at the NHLH2 Core Promoter Exceptionally Long CA-Repeat in Human and Disease-Only Genotypes in Late-Onset Neurocognitive Disorder. Gerontology 2020; 66:514-522. [PMID: 32877896 DOI: 10.1159/000509471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/17/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Approximately 2% of the human core promoter short tandem repeats (STRs) reach lengths of ≥6 repeats, which may in part be a result of adaptive evolutionary processes and natural selection. A single-exon transcript of the human nescient helix loop helix 2 (NHLH2) gene is flanked by the longest CA-repeat detected in a human protein-coding gene core promoter (Ensembl transcript ID: ENST00000369506.1). NHLH2 is involved in several biological and pathological pathways, such as motivated exercise, obesity, and diabetes. METHODS The allele and genotype distribution of the NHLH2 CA-repeat were investigated by sequencing in 655 Iranian subjects, consisting of late-onset neurocognitive disorder (NCD) as a clinical entity (n = 290) and matched controls (n = 365). The evolutionary trend of the CA-repeat was also studied across vertebrates. RESULTS The allele range was between 9 and 25 repeats in the NCD cases, and 12 and 24 repeats in the controls. At the frequency of 0.56, the 21-repeat allele was the predominant allele in the controls. While the 21-repeat was also the predominant allele in the NCD patients, we detected significant decline of the frequency (p < 0.0001) and homozygosity (p < 0.006) of this allele in this group. Furthermore, 12 genotypes were detected across 16 patients (5.5% of the entire NCD sample) and not in the controls (disease-only genotypes; p < 0.0003), consisting of at least one extreme allele. The extreme alleles were at 9, 12, 13, 18, and 19 repeats (extreme short end), and 23, 24, and 25 repeats (extreme long end), and their frequencies ranged between 0.001 and 0.04. The frequency of the 21-repeat allele significantly dropped to 0.09 in the disease-only genotype compartment (p < 0.0001). Evolutionarily, while the maximum length of the NHLH2 CA-repeat was 11 repeats in non-primates, this CA-repeat was ≥14 repeats in primates and reached maximum length in human. CONCLUSION We propose a novel locus for late-onset NCD at the NHLH2 core promoter exceptionally long CA-STR and natural selection at this locus. Furthermore, there was indication of genotypes at this locus that unambiguously linked to late-onset NCD. This is the first instance of natural selection in favor of a predominantly abundant STR allele in human and its differential distribution in late-onset NCD.
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Affiliation(s)
- Hossein Afshar
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Adelirad
- Department of Health Education and Promotion, Faculty of Health Sciences Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Kowsari
- Department of Mesenchymal Stem Cell, The Academic Center for Education, Culture and Research, Qom, Iran
| | - Naser Kalhor
- Department of Mesenchymal Stem Cell, The Academic Center for Education, Culture and Research, Qom, Iran
| | - Ahmad Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Najafipour
- Cellular and Molecular Research Centre, Research Institute for Prevention of Non Communicable Disease, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mahshid Foroughan
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Ali Bozorgmehr
- Department of Neuroscience, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Safoura Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Neda Nazaripanah
- Department of Health Education and Promotion, Faculty of Health Sciences Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mina Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran,
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Abstract
BACKGROUND Short tandem repeats (STRs) contribute significantly to de novo mutagenesis, driving phenotypic diversity and genetic disease. Although highly diverse, their repetitive sequences induce DNA polymerase slippage and stalling, leading to length and sequence variation. However, current studies of DNA synthesis through STRs are restricted to a handful of selected sequences, limiting our broader understanding of their evolutionary behaviour and hampering the characterisation of the determinants of their abundance and stability in eukaryotic genomes. RESULTS We perform a comprehensive analysis of DNA synthesis at all STR permutations and interrogate the impact of STR sequence and secondary structure on their genomic representation and mutability. To do this, we developed a high-throughput primer extension assay that allows monitoring of the kinetics and fidelity of DNA synthesis through 20,000 sequences comprising all STR permutations in different lengths. By combining these measurements with population-scale genomic data, we show that the response of a model replicative DNA polymerase to variously structured DNA is sufficient to predict the complex genomic behaviour of STRs, including abundance and mutational constraints. We demonstrate that DNA polymerase stalling at DNA structures induces error-prone DNA synthesis, which constrains STR expansion. CONCLUSIONS Our data support a model in which STR length in eukaryotic genomes results from a balance between expansion due to polymerase slippage at repeated DNA sequences and point mutations caused by error-prone DNA synthesis at DNA structures.
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Affiliation(s)
- Pierre Murat
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Guillaume Guilbaud
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Julian E Sale
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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Chen Z, Xuan Y, Liang G, Yang X, Yu Z, Barker SC, Kelava S, Bu W, Liu J, Gao S. Precise annotation of tick mitochondrial genomes reveals multiple copy number variation of short tandem repeats and one transposon-like element. BMC Genomics 2020; 21:488. [PMID: 32680454 PMCID: PMC7367389 DOI: 10.1186/s12864-020-06906-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 07/10/2020] [Indexed: 02/07/2023] Open
Abstract
Background In the present study, we used long-PCR amplification coupled with Next-Generation Sequencing (NGS) to obtain complete mitochondrial (mt) genomes of individual ticks and unprecedently performed precise annotation of these mt genomes. We aimed to: (1) develop a simple, cost-effective and accurate method for the study of extremely high AT-content mt genomes within an individual animal (e.g. Dermacentor silvarum) containing miniscule DNA; (2) provide a high-quality reference genome for D. silvarum with precise annotation and also for future studies of other tick mt genomes; and (3) detect and analyze mt DNA variation within an individual tick. Results These annotations were confirmed by the PacBio full-length transcriptome data to cover both entire strands of the mitochondrial genomes without any gaps or overlaps. Moreover, two new and important findings were reported for the first time, contributing fundamental knowledge to mt biology. The first was the discovery of a transposon-like element that may eventually reveal much about mechanisms of gene rearrangements in mt genomes. Another finding was that Copy Number Variation (CNV) of Short Tandem Repeats (STRs) account for mitochondrial sequence diversity (heterogeneity) within an individual tick, insect, mouse or human, whereas SNPs were not detected. The CNV of STRs in the protein-coding genes resulted in frameshift mutations in the proteins, which can cause deleterious effects. Mitochondria containing these deleterious STR mutations accumulate in cells and can produce deleterious proteins. Conclusions We proposed that the accumulation of CNV of STRs in mitochondria may cause aging or diseases. Future tests of the CNV of STRs hypothesis help to ultimately reveal the genetic basis of mitochondrial DNA variation and its consequences (e.g., aging and diseases) in animals. Our study will lead to the reconsideration of the importance of STRs and a unified study of CNV of STRs with longer and shorter repeat units (particularly polynucleotides) in both nuclear and mt genomes.
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Affiliation(s)
- Ze Chen
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, P. R. China
| | - Yibo Xuan
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, P. R. China.,College of Life Sciences, Nankai University, Tianjin, Tianjin, 300071, P. R. China
| | - Guangcai Liang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, Tianjin, 300350, P. R. China
| | - Xiaolong Yang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, P. R. China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, P. R. China
| | - Stephen C Barker
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Samuel Kelava
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Wenjun Bu
- College of Life Sciences, Nankai University, Tianjin, Tianjin, 300071, P. R. China
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, P. R. China.
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, Tianjin, 300071, P. R. China. .,School of Statistics and Data Science, Nankai University, Tianjin, Tianjin, 300071, P. R. China.
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42
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Wu R, Peng D, Ren H, Li R, Li H, Wang N, Shen X, Huang E, Zhang Y, Sun H. Characterization of genetic polymorphisms in Nigerians residing in Guangzhou using massively parallel sequencing. Forensic Sci Int Genet 2020; 48:102323. [PMID: 32574994 DOI: 10.1016/j.fsigen.2020.102323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/21/2020] [Accepted: 06/03/2020] [Indexed: 01/13/2023]
Abstract
African populations exhibit extensive linguistic and cultural diversity but are less studied from a population genetic standpoint. Although much genetic data on admixed African individuals, such as African Americans, have been published, genetic polymorphism data, especially that based on sequence-based typing, are still insufficient in indigenous Africans. In this study, we examined the genetic diversity of 85 Nigerians residing in Guangzhou, China. Forensically relevant genetic markers, including autosomal short tandem repeats (A-STRs), X-chromosomal STRs (X-STRs), Y-chromosomal STRs (Y-STRs), and identity-informative single nucleotide polymorphisms (iiSNPs) were genotyped to uncover the genetic polymorphisms of this population. Sequence-based allelic variations were observed in 22 A-STRs, ten Y-STRs, and four X-STRs. Using massively parallel sequencing (MPS), the allele number increased from 475 length-based alleles to 683 sequence-based alleles. Compared to other populations, the overall observed heterozygosity of the 27 A-STRs was the highest in Nigerians, which reflected the higher genetic diversity of this population. The combined match probability of the 27 A-STRs was low at 9.06 × 10-38. When both A-STRs and iiSNPs were considered, the cumulative discrimination power, and combined power of exclusion for duo and trio paternity testing was 1-2.97 × 10-57, 1-2.20 × 10-10 and 1-4.61 × 10-17, respectively, which demonstrated that the STRs and SNPs analyzed here can be applied to forensic investigations. In summary, this study uncovers the genetic features of the Nigerian population and provides valuable frequency data for forensic applications.
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Affiliation(s)
- Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Han Ren
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Ran Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Haixia Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Nana Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Xuefeng Shen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Erwen Huang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China.
| | - Yinming Zhang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China.
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China.
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43
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Yang X, Xu Q, Liu Q, Liu C, Hu H, Han X, Chen L, Liu C. Combined application of multiple autosomal and Y-chromosomal STR loci in solving a homicide case in 2009. Int J Legal Med 2020; 135:755-760. [PMID: 32468171 DOI: 10.1007/s00414-020-02322-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/20/2020] [Indexed: 10/24/2022]
Abstract
In 2009, a violent murder occurred. Two victims, a 47-year-old mother and her 21-year-old daughter, were murdered at home. After importing the 20 autosomal STR loci and 27 Y-STR loci into a database, no hit had been found. In 2019, a person with a prior criminal record was matched in the national forensic Y-STR database. When increasing the number of detected Y-STR loci to 60, all loci of the bloodstain donor at the crime and the suspect were still found to be identical. With the combined calculation of multiple autosomal STR and kinship index, we were able to identify the perpetrator as a previously unknown illegitimate child of a large family and solved the case.
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Affiliation(s)
- Xingyi Yang
- Guangzhou Forensic Science Institute, Guangzhou, People's Republic of China
| | - Quyi Xu
- Guangzhou Forensic Science Institute, Guangzhou, People's Republic of China
| | - Qi Liu
- Tianhe Branch of Guangzhou Public Security Bureau, Guangzhou, People's Republic of China
| | - Changhui Liu
- Guangzhou Forensic Science Institute, Guangzhou, People's Republic of China
| | - Huiying Hu
- Guangzhou Forensic Science Institute, Guangzhou, People's Republic of China
| | - XiaoLong Han
- Guangzhou Forensic Science Institute, Guangzhou, People's Republic of China
| | - Ling Chen
- Department of forensic Medicine, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Chao Liu
- Guangzhou Forensic Science Institute, Guangzhou, People's Republic of China.
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44
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Kobayashi M, Yusa Y, Sekino M. Microsatellite DNA markers applicable to paternity inference in the androdioecious gooseneck barnacle Octolasmis warwickii (Lepadiformes: Poecilasmatidae). Mol Biol Rep 2020; 47:4885-4890. [PMID: 32378167 DOI: 10.1007/s11033-020-05473-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/25/2020] [Indexed: 11/26/2022]
Abstract
The gooseneck barnacle Octolasmis warwickii has a rare sexual system called androdioecy, in which hermaphrodites and dwarf males co-occur. It has been hypothesized that dwarf males can coexist with conspecific hermaphrodites when dwarf males are capable of leaving more offspring than hermaphrodites via male reproduction. This hypothesis of reproductive superiority of dwarf males can be validated by comparing the reproductive success between dwarf males and hermaphrodites through DNA marker-based parentage testing. In the present study, we developed microsatellite DNA markers for O. warwickii, and evaluated the power of these markers to infer parentage based on simulation analysis. Using next generation sequencing, we obtained 344 microsatellite sequences suitable for designing primer sets for amplification in polymerase chain reaction (PCR). Of these, we examined the PCR amplification efficiency of 54 primer sets, of which 11 passed our primer screening in a population sample (n = 35). The developed markers exhibited moderate to high levels of polymorphisms, and met Hardy-Weinberg equilibrium with little evidence of significant allelic association to each other. Our simulated paternity inference suggested that the combinational use of the markers allows a high resolution of parentage (success rate of > 99.9%) if all candidate fathers are available.
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Affiliation(s)
- Mayumi Kobayashi
- National Research Institute of Fisheries Science, Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yoichi Yusa
- Division of Natural Sciences, Nara Women's University, Nara, Japan
| | - Masashi Sekino
- National Research Institute of Fisheries Science, Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan.
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45
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Nishi T, Fukui K, Iwadate K. Genetic polymorphism analyses of three novel X chromosomal short tandem repeat loci in the Xp22.3 region. Leg Med (Tokyo) 2020; 45:101709. [PMID: 32371301 DOI: 10.1016/j.legalmed.2020.101709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/13/2020] [Accepted: 04/17/2020] [Indexed: 11/18/2022]
Abstract
X chromosomal short tandem repeats (X-STRs) can be useful for haplotype analysis in DNA testing, particularly for complex kinship testing or when one parent is absent. We searched downstream of four previously detected loci in the Xp22.3 region (LC149476, LC149479, LC149480, and LC149484) and detected and analyzed three novel short tandem repeats (STRs), LC317283, LC317284, and LC317285, with the repeat sequences TATAA, TTTA, and TATC, respectively. The forensic statistical values in Japanese subjects were confirmed to be noninferior to existing loci, with values for polymorphism information content, the power of discrimination in males (PDm), and the power of discrimination in females (PDf) of 0.5606-0.7448, 0.6078-0.7774, and 0.7990-0.9178, respectively. Haplotype analysis also revealed linkage disequilibrium between LC317283 and the four known loci (LC149476, LC149479, LC149480, and LC149484) and between two other novel loci (LC317284 and LC317285). Analysis of three family samples suggested that these STRs could be useful in complex kinship testing, so we developed an X-STR multiplex polymerase chain reaction (PCR) system for the seven loci and confirmed its ability to provide favorable amplification. We anticipate that the identified loci and developed multiplex PCR system will be beneficial to the field of forensic medicine.
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Affiliation(s)
- Takeki Nishi
- Department of Forensic Medicine, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, 105-8461 Tokyo, Japan.
| | - Kenji Fukui
- Department of Forensic Medicine, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, 105-8461 Tokyo, Japan
| | - Kimiharu Iwadate
- Department of Forensic Medicine, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, 105-8461 Tokyo, Japan
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46
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Iarussi F, Cipolloni L, Bertozzi G, Sasso L, Ferrara M, Salerno M, Rubino GTR, Maglietta F, Dinisi A, Albano D, Iarussi V, Pomara C, Sessa F. Dog-bite-related attacks: A new forensic approach. Forensic Sci Int 2020; 310:110254. [PMID: 32200306 DOI: 10.1016/j.forsciint.2020.110254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 03/04/2020] [Accepted: 03/11/2020] [Indexed: 11/22/2022]
Abstract
Dog attacks today represent a health hazard considering that prevention strategies have not always been successful. The identification of the dog that attacked the victim is necessary, considering the civil or criminal consequences for the animal's owner. An accurate scene analysis must be performed collecting a series of important information. Forensic investigations in dog attacks involve different methods, such as the evaluating of the canine Short Tandem Repeat (STR) typing in saliva traces on wounds or bite mark analysis, however, these techniques cannot always be applied. The effort to find new methods to identify the dog that attacked the victim represents a very interesting field for the forensic community. This study aims to propose an innovative approach, based on the identification of the victim's profile in the dog's mouth, using a buccal swab on the suspected aggressor dog, to find the victim's genetic profile. In addition, a further goal of this study is to determine the persistence time of hexogen DNA in the dog's mouth to define a timeframe for performing this particular technique. For this purpose, ten different dogs were used to aggressively bite a bovine sample (reference sample) to simulate the victim. For each dog two buccal swabs were taken at different time intervals: 30', 45', 60', 90', 120', 150', 180' and 240'. The typing of the swabs provided an interpretable profile after 45' while traces of bovine profile were found until 150' after the dog attack simulation. These results could be improved using the human identification kit, which is more sensitive. In the light of this experimental study, the forensic community should consider using this approach in real casework studies with the aim of collecting new data, validating this technique for forensic use.
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47
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Shortreed CG, Wiseman RW, Karl JA, Bussan HE, Baker DA, Prall TM, Haj AK, Moreno GK, Penedo MCT, O'Connor DH. Characterization of 100 extended major histocompatibility complex haplotypes in Indonesian cynomolgus macaques. Immunogenetics 2020; 72:225-239. [PMID: 32112172 PMCID: PMC7223175 DOI: 10.1007/s00251-020-01159-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/04/2020] [Indexed: 12/21/2022]
Abstract
Many medical advancements—including improvements to anti-rejection therapies in transplantation and vaccine development—rely on preclinical studies conducted in cynomolgus macaques (Macaca fascicularis). Major histocompatibility complex (MHC) class I and class II genes of cynomolgus macaques are orthologous to human leukocyte antigen complex (HLA) class I and class II genes, respectively. Both encode cell-surface proteins involved in cell recognition and rejection of non-host tissues. MHC class I and class II genes are highly polymorphic, so comprehensive genotyping requires the development of complete databases of allelic variants. Our group used PacBio circular consensus sequencing of full-length cDNA amplicons to characterize MHC class I and class II transcript sequences for a cohort of 293 Indonesian cynomolgus macaques (ICM) in a large, pedigreed breeding colony. These studies allowed us to expand the existing database of Macaca fascicularis (Mafa) alleles by identifying an additional 141 MHC class I and 61 class II transcript sequences. In addition, we defined co-segregating combinations of allelic variants as regional haplotypes for 70 Mafa-A, 78 Mafa-B, and 45 Mafa-DRB gene clusters. Finally, we defined class I and class II transcripts that are associated with 100 extended MHC haplotypes in this breeding colony by combining our genotyping analyses with short tandem repeat (STR) patterns across the MHC region. Our sequencing analyses and haplotype definitions improve the utility of these ICM for transplantation studies as well as infectious disease and vaccine research.
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Affiliation(s)
- Cecilia G Shortreed
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Roger W Wiseman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA.,Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Julie A Karl
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Hailey E Bussan
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - David A Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Trent M Prall
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Amelia K Haj
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Gage K Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | | | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA. .,Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA.
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48
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Fortschegger M, Preuner S, Printz D, Poetsch AR, Geyeregger R, Pichler H, Lawitschka A, Lion T. Detection and Monitoring of Lineage-Specific Chimerism by Digital Droplet PCR-Based Testing of Deletion/Insertion Polymorphisms. Biol Blood Marrow Transplant 2020; 26:1218-1224. [PMID: 32092354 DOI: 10.1016/j.bbmt.2020.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/03/2020] [Accepted: 02/13/2020] [Indexed: 12/31/2022]
Abstract
Analysis of specific leukocyte subsets for post-transplantation monitoring of chimerism provides greater sensitivity and clinical informativeness on dynamic changes in donor- and recipient-derived cells. Limitations of the most commonly used approach to chimerism testing relying on PCR-based analysis of microsatellite markers prompted us to assess the applicability of digital droplet (dd) PCR amplification of deletion/insertion polymorphisms (DIPs) for lineage-specific chimerism testing in the related stem cell transplantation setting, where the identification of informative markers facilitating the discrimination between donor-derived and recipient-derived cells can be challenging. We analyzed 100 genetically related patient-donor pairs by ddPCR analysis using commercially available DIP kits including large sets of polymorphic markers. At least 1 informative marker was identified in all related pairs analyzed, and 2 or more discriminating markers were detected in the majority (82%) of instances. The achievable detection limit is dependent on the number of cells available for analysis and was as low as 0.1% in the presence of ≥20,000 leukocytes available for DNA extraction. Moreover, the reproducibility and accuracy of quantitative chimerism analysis compared favorably to highly optimized microsatellite assays. Thus, the use of ddPCR-based analysis of DIP markers is an attractive approach to lineage-specific monitoring of chimerism in any allogeneic transplantation setting.
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Affiliation(s)
| | - Sandra Preuner
- St Anna Children's Cancer Research Institute, Vienna, Austria
| | - Dieter Printz
- St Anna Children's Cancer Research Institute, Vienna, Austria
| | - Anna R Poetsch
- St Anna Children's Cancer Research Institute, Vienna, Austria
| | - René Geyeregger
- St Anna Children's Cancer Research Institute, Vienna, Austria
| | | | | | - Thomas Lion
- St Anna Children's Cancer Research Institute, Vienna, Austria; Department of Pediatrics, Medical University of Vienna, Vienna, Austria.
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49
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Wang Z, Wang L, Liu J, Ye J, Hou Y. Characterization of sequence variation at 30 autosomal STRs in Chinese Han and Tibetan populations. Electrophoresis 2020; 41:194-201. [PMID: 31916267 DOI: 10.1002/elps.201900278] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/25/2019] [Accepted: 12/08/2019] [Indexed: 11/11/2022]
Abstract
Massively parallel sequencing (MPS) technologies have the ability to reveal sequence variations within STR alleles as well as their nominal allele lengths, which have traditionally been detected by CE instruments. Recently, Thermo Fisher Scientific has updated the MPS-STR panel, named the Precision ID GlobalFiler next-generation sequencing (NGS) STR Panel version 2, with primers redesigned to add two pentanucleotide tandem repeat loci and profile interpretation supported by the Converge software. Using the Ion Chef System, the Ion S5XL System, and the Converge software, genetic variations were characterized within STR repeat and flanking regions of 30 autosomal STR markers in 115 unrelated individuals from two Chinese population groups (58 Tibetans and 57 Hans). Nineteen STRs demonstrated a relative increase in diversity with the variant sequence alleles compared with those of traditional nominal length alleles. In total, 390 alleles were identified by their sequences compared with 258 alleles that were identified by length. Of these 92 sequence variants found within the STR repeat regions, 40 variants were located in STR flanking regions. Additionally, the agreement of the results with CE data was evaluated, as was the ability of this new MPS panel to analyze case-type (11 samples) and artificially degraded samples (seven samples in triplicate). The results generated from this study illustrate that extensive sequence variation exists in commonly used STR markers in the selected population samples and indicate that this NGS STR panel has the potential to be used as an effective tool for human forensics.
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Affiliation(s)
- Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Le Wang
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Jian Ye
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China.,Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
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50
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Lin L, Li J, Hu Y, Wang H, Marah FA, Moseray M, Kureshi A, Wang C, Zeye MMJ, Zha L. Genetic characterization of 19 X-STRs in Sierra Leone population from Freetown. Int J Legal Med 2020; 134:1659-1661. [PMID: 31897669 DOI: 10.1007/s00414-019-02243-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 12/19/2019] [Indexed: 11/26/2022]
Abstract
A total of 550 individuals (265 males and 285 females) from Sierra Leone, a west-African coastal country, were genotyped using the Microreader™ 19X ID System kit. No significant deviations from the Hardy-Weinberg equilibrium were observed. A total of 250 alleles were identified with corresponding allele frequencies spanning from 0.0012 to 0.6762. PIC of the loci ranged from 0.4615 to 0.9481. The CPE, CPDF, and CPDM were 0.9999997856, 0.999999999999999999995774, and 0.999999999998997, respectively. The highly combined MECKruger, MECKishida, MECDesmarais, and MECDesmarais Duo were achieved as 0.99999992508, 0.999999999990802, 0.999999999990836, and 0.99999998412, respectively. Genetic comparisons revealed that genetic homogeneity existed in similar ethno origin or geographic origin populations. This is a pioneering genetic investigation using the Microreader™ 19X ID System kit in the population of Sierra Leone.
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Affiliation(s)
- Lin Lin
- Xiangya Hospital, Central South University, No87. Xiangya Road, Changsha, Hunan, People's Republic of China
- Reproductive Medicine Center, Fujian Provincial Maternity and Children's Hospital, No18. Daoshan Road, Fuzhou, Fujian, People's Republic of China
| | - Jienan Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China
| | - Yize Hu
- Wuxi Municipal Public Security Bureau, Wuxi, Jiangsu, People's Republic of China
| | - Han Wang
- Department of Clinical Diagnostic Centre, the Fifth Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing, People's Republic of China
| | - Foday Ambrose Marah
- The GREY Bush Community Health Center, Grey Bush, Ascension-town, Sierra Leone
| | - Moses Moseray
- Joint Medical Unit, Freetown, Sierra Leone
- Clinical Laboratory, 34 Military hospital, Freetown, Sierra Leone
| | - Aliye Kureshi
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China
| | - Chudong Wang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China
| | - Moutanou Modeste Judes Zeye
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China
- Laboratory of Molecular Biology and Genetics (LMBG), University Joseph KI - ZERBO, CERBA/LABIOGENE, 01 BP 364, Ouagadougou 01, Burkina Faso
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan Province, People's Republic of China.
- China-Africa Research Center of Infectious Deseases, Central South University, Changsha, People's Republic of China.
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